Shinobi: Second Evolution
by The Phantom Penance
Summary: He was a clone of the most strongest shinobi that ever existed, and the last shinobi that fell in that time. Back then, he protected his loved ones from any who threatened them, now, he'll protect his fellow mutants from those who would seek to destroy them. Brace yourself, they will definitely come in all different shape and sizes!
1. Chapter 1

**Hello readers! This the Phantom Penance, and I have returned with a whole new fic!**

 **I may not be as frequent with this one as opposed to the man others I have been working on because they're all long term fanfics and it's really hard to juggle them one at a time.**

 **But this one…has been boiling in my mind since March, so I'd thought I'd get a move on it.**

 **First Naruto and X-Men fanfic I HAVE EVER MADE, TELL ME HOW YOU GUYS LIKE IT! (DISCLAIMER: I OWN NOTHING)**

* * *

 **SECOND SIGHT**

 **Chapter 1: Fall of the Leaf**

 _To the one who finds this journal, this is a safety measure in case our plans are foiled and we have somehow managed to lose our precious memory, it is placed to remind you who you are and what your purpose is in life. Our name is En Sabah Nur, or the First One in the common tongue. We have spent many nights in the harsh void that was the desert and survived it, better yet, we became its rightful master._

 _We are the kings of the desert and everyone who thrives on it because of one singular reason: we posses the powers of a god, WE are a god. Opposition and weakness was not and will not be tolerated in our kingdom because like the desert itself, only the strong shall be granted the precious gift of life in our rule._

 _Recently, I had discovered a new ability that we had amassed through the combination of our divine power and technology, we were virtually impenetrable to the throes of time. This knowledge had further cemented my belief that I alone was destined to rule, to lead only the worthy to a brighter future free from weakness and pain, but it was in my moment of triumph did I realize a lingering truth:_

 _I may never age, but I am still very much capable of being slain in combat. The chance of that ever happening was astronomically small, but fortune favors the prepared, as I have learned in life. I now knew what I had to do in life, to find true immortality and secure myself as the strongest being in existence._

 _My search had taken me to many strange places, far from the death of the desert that was my home and into lush planes of paradise until I had stumbled across something promising. An entire civilization of warriors with capabilities like ourself in the most isolated corner of the world._

 _Their abilities ranged in many different forms and fashions, if I were a weaker being, I would admit that it was beautiful in a way, but I knew that these….inferiors were playing god in the midst of a REAL god, nevertheless, they may contain the immortality I seek._

 _Thus, I begun my Collection phase: to collect their abilities and study them in hopes of making a real elixir of life. Of course, the only safe way to do that was to conquer everything._

 _As the First One commanded, so it was._

* * *

The conquest was slow and painful, he had to admit that these…..shinobi were quite determined to protect their little lives, but they foolishly challenged a force of nature. Nothing can stop the Sandstorm of death that entrapped them.

Their army were of men with superhuman capabilities whereas his was of metal and more were being manufactured to counteract their abilities.

And where was he? Sitting upon his throne in his protected Spire, not that he needed his army to protect him, they protected his growing library of samples.

The First One was currently studying the five most prized samples of his collection, coincidentally, blood and organs of the only five ants that dared to attack him head on. His favorite of the five was one of a woman who healed from his attacks at a remarkable rate, something he felt would be a cornerstone to his research of immortality, but regrowing organs seemed to be too much for her, like her heart when he ripped it out.

The other was of a red head who used the will of the sand to attack for him. The First One was impressed that someone could control something so merciless like that of the sand, so he kept his blood and the brain, he felt that the brain was the source of his power.

The other three were impressive as well. The one who can compose his body out of lighting, the old man who can fly, and a woman who spits out fire and molten rock. All very impressive, but lacking what he needs to complete his quest for immortality.

"Great One," The First lowered his eyes to see one of his metal soldiers bowing down to him, no doubt to give him a report of the battle that enraged outside.

"The remaining fighters have surrounded themselves in the forest areas, destroying any units that try to begin the deforestation process." The robot reported in a mechanized voice.

They wanted to run and hide from him? Try to lengthen the inevitable? The nerve of those ingrates! How dare they disrespect him like that! In rage, the First One's fingers broke through the hard surface of his throne as he stood.

"Open the main door!" He bellowed as he curled and uncurled his left hand repeatedly. "If these spineless cowards will not face me head-on in battle, then they will feel the terrible power of my wrath!"

He left his home and floated across a dead land. What was flourishing in foliage and wildlife was burnt, torn asunder, and ruined by hundreds of dead bodies rotting on the ground. The First One floated above the end of the waste to see a workforce of metal standing closely side-to-side as they slowly cut down the massive trees that loomed high above.

"Master," The commanding machine addressed The First One when he landed to the soil, "You need not concern yourself with this. We have the situation under-"

The robot squawked as circuitry were ripped apart and metal was torn until its head completely separated from its body and floated gently into the hands of The First One.

"None may tell me what I place my concerns, least of all, a weak automaton that I constructed myself." He replied to the headless robot.

He turned to the trees and slowly began to raise his left hand, and as he did, the ground beneath the forest began to break, to shuffle, to grind into dirt, and eventually, rise. Those machines that could began to quickly back away from the rising ground and the roots that were being uprooted.

The First One lifted up his second hand to pick up the entire forest in front of him and to raise it into the sky until he and his army could see massive walls made of wood and a mountain behind it.

Then he dropped the forest.

The trees and the earth fell silently until it reunited with the ground in a sound like the combined forces of thunder and a massive sandstorm. The ground shook violently like that of an earthquake and many of The First One's machines were crushed beneath the falling boulders and the sand. Nothing that could not be replaced.

When the dust settled, the trees were all crushed and uprooted, but the village laid in his sights at last.

"AS CONQUEROR, I COMMAND THAT YOUR LEADER STOPS HIDING BEHIND HIS PITIFUL WALLS AND FACE ME NOW!" He bellowed in a magnified voice at the village. Silence was his response until the walls groaned their way open and a lone figure approached.

The First One raised an eyebrow as he floated to meet the supposed leader half way from the village. With the power of gravity, he willed a circle of earth to rise from the ground so that he could talk to his guest away from the destruction of the forest.

The First One stood two heads taller than his…..unusual guest. It was a man with unruly hair that was silver, he also had an eyepatch with an insignia grafted onto a metal piece attached to said eyepatch, he wore a mask that concealed the lower half of his face and dark grey armor.

"After your little performance with our trees, I figured those walls weren't going to do much." The man spoke in a lazy and uncaring tune, something that was going to quickly annoy The First One.

"So now you realize that it is pointless to hide from me," He replied to the silver haired man.

"We weren't hiding, just stalling time so that our people could get to a safe location away from all of….this." The man explained while placing his hands in his pockets.

"Bah! I care little for those weaklings!" The First One spat in annoyance.

The man shrugged his shoulders, as if to say he didn't care what the giant of a man wanted. "Great, now that we're at this subject, care to explain why you're trying to kill us?"

"I am attempting to conquer this land, you are resisting" The First One explained, "however, your continued resistance to defy me-as fruitless as it is- has impressed me to a degree. I shall offer you terms for surrender: you and every one of your soldiers will submit to my rule and I will grant them life, a very reasonable offer coming from me."

The silver-haired man nodded in consideration before he asked, "And what of the children and the injured, those who can't fight?"

The First One scowled, "Their fates will be determined by me. There is no weakness in my reign. Make a decision now, for my patience with this pointless struggle is at an end."

* * *

 _He refused._

 _Had this….Kakashi knew what he was dealing with, he might have reconsidered, but I do not give second chances. Little did I know, he had been using that temporary moment of peace to position his men and attempt to attack my army by surprise._

 _I'll admit, the battle was impressive. He held a mastered degree over the basic elements and was able to conjure a massive behemoth, but it was nothing I had not seen before with the other one I met. He was all alone and was in possession of an unique purple eye with rings in it. I still have that eye, as a spoil of war._

 _But in the end, I absorbed that man's power and sliced off his head personally. I had thought that by killing their leader, the other soldiers would lose moral and surrender easily, but it seemed that they did not rally to him. Their battle cry was of this Will of Fire, I perceived it as the will to survive at first, but it was later interpreted for me as the will to protect others._

 _Ignorant fools, all of them. It was meaningless to defend someone who didn't have the stomach to defend themselves, I showed them firsthand that no fire could stand against the might of one who has mastered the will of the desert, the truth that the strongest shall survive, and the weak fall._

 _But the Hidden Leaf village held one last champion._

 _I will unashamedly admit that he was the mightiest foe I had ever faced, perhaps ever will face, and our battle was on a proportion that barely I could imagine. He had been waiting all along for when my army was on the verge of destroying the doors to his village, when the gate fell to the ground…_

* * *

The First One spun back around when he heard a massive explosion. An energy of orange was tearing through his machines faster than anything he had ever seen.

"What is-"

He couldn't finish his question as brute force broke through his shields and pummeled him deep into the earth. He gritted his teeth as this massive force punched him farther and farther away from his troops and the village.

It left him to crawl out of the crater they had made, he growled as he dusted his armor of the dirt.

"Who dares to touch me!?"

" **I do."** He spun around and faced the owner of the dark voice, but once he did, The First One felt deep inside him something that of kinship, that he had found someone who had also went through a desert of their own and became a god.

It was a young man, but his entire body glowed like that of a celestial. His face was yellow like the short jacket he wore and the rest of his attire was blacker than night. His eyes were slits and several black orbs floated behind him.

' _T-This boy….has he become a god like me?'_ Were the thoughts that echoed in The First One's mind as he stared on in wonder at his new opponent.

"You killed Lee, Choji, Kiba, Tenten, you killed my friends!" The boy growled as he gripped his dark rods in pure rage.

Despite the circumstances that confronted him, En Sabah did something he did not do in a long time: he laughed. Genuinely laughed. He laughed at the boy, for the boy, for no apparent reason at all it seemed. He just laughed.

The boy however, took it as something else. "You think that's funny huh!?"

Eventually, The First One suppressed his laughter to and resumed his normal self, "What is your name, boy?"

The spiky haired warrior remained unfazed as he answered. "Naruto Uzumaki, the Child of Prophecy, soon-to-be Seventh Hokage of the Hidden Leaf, and your end!"

"You're quite certain of that, aren't you boy?" The First One smirked while he folded his hands. "I'll admit, the element of surprise was yours with that first attack, but you posses nothing that can come close to-"

Before he could even blink, the boy's fist was in his face.

He staggered back and then found the fists in his chest, then under his chin, then a foot in his back. The glowing brat was moving in a speed that the First One could not even comprehend! His attacks were fast and strong, throwing him back and forth in whatever direction the boy would hit him.

" **ODAMA RASENGAN!"** The First One grunted as he felt something-massive!- try to grind his back into bloody meat. The force of this giant ball drove him deep into the earth, deep enough to form a crater.

Rubble cleared away so Naruto could get a good look at his opponent, to his surprise, a hand that was twice his size grabbed the edge of the crater and a body that was growing at an incredulous rate loomed above him.

"An impressive attempt, but for naught." The First One's voice boomed down to his ant-sized opponent. "My armor is composed of the rarest materials known in history. Mere brute strength cannot destroy it or me."

Suddenly, the boy started to grow an avatar made of the same power that encompassed his own body until The First One stared in amazement at a fox-like creature with nine tails and three arms that stood directly at the same level as he.

First he was amazed, then he steadily grew into a rage, "You….brat! NO ONE COMPARES TO ME!"

He punched the creature straight into the jaw. The fox avatar stumbled back a little before landing three blows on The First One. The fox was full of ferocity, he kept landing blow after blow despite being uncapable of even denting the armor he pounded against.

The First One was equally unsuccessful and that was starting to send him into a fury. The avatar was composed of extremely dense energy that stood against each and every one of his attacks, they were locked into battle that was leveling the earth beneath them and neither of them possessed the power to escape it.

"MISERABLE BRAT!" The First One roared in rage. He backed away from the boy and willed his body to form a mechanism, a massive gun, from his chest and arms. The cannon whirred and charged up powerful energy as a purple light shined down the hole of the cannon.

"DIE!" With that, he fired a beam of pure energy. It leveled the ground beneath them as it soared to the unmoving fox avatar. The boy inside it gritted his teeth as the fox held all six of its arms in front of its face for protection.

The energy slammed into the fox with enough force to tear the earth apart. The First One stared in satisfaction as his enemy attempted to block the attack before he exploded, such was the fate of those who dared to challenge a god.

Contented, he turned from the remains of his opponent and began to walk back to his Spire. The machines were well equipped to handle any stragglers that were foolish to fight-

" **Wind Style!"**

"Impossible!" The First One snarled as he spun around. The boy was indeed alive, and what's more, _he was going to return the favor._

The Fox was crouched on all fours (since he has six arms, technically all eights) with four hands to handle the massive blob of black energy that was about to cover its entire back and it was growing fast.

" **Ultra Big Tailed Beast Bomb Rasenshuriken!"**

The fox threw the massive black projectile with all its might, the ball flew a couple of feet (probably miles due to their size) before it expanded to become even bigger. The First One yelled out when he tried to stop it with his own hands.

Despite his near invincibility, the force of the ball was turning his hands into fire, his feet dug into the ground as the mere power of the giant black ball forced him farther and farther back.

"I-WILL-NOT-ACCEPT THIS!" He roared and reached deep inside him to find the power necessary to survive, and he did. With a mighty yell of rage, desperation, he sent the attack right back at the fox. The fox merely ducked underneath the ball, but that was fatal mistake. The massive ball soared farther and farther behind him till it finally impacted something.

The giant Mountain with the five faces.

The explosion was massive, even for their gigantic size.

The fox instantly knew what was wrong and turned around, only to find his precious home reduced to a giant cloud mushroom and fire. The First One assumed that the boy began to think that he had destroyed his home and everyone that lived in it since he started to shrink back into his base form, with The First One following suit.

He stared with satisfaction as the boy fell onto his knees and began to mumble something, most likely the names of those he had obliterated, their blood on his hands.

"I did not expect this outcome to come into play, and I am pleased with that." The First One declared as he walked up right behind the boy. "In the end, I did not annihilate the last of your people, you did that for me. I express my gratitude, but it is time for me to finish this prattle."

The boy roared as he spun around, only to find a massive hand on his head and The First One entering his mind. The First One raised an eyebrow as he stared at the puddle of water that surrounded him before looking up at the massive, orange, fox with nine tails.

"So you are the source of this brat's power," He spoke to the snarling fox before spitting to the ground. "As I thought, my only true equal in battle turns out to be a mere parasite to true power."

" **I'll grind you into dust!"** The beast roared as it tried to stab him with its giant nail, but the astral projection of The First One phased harmlessly through it.

"It's clear that I can't kill something of your origin. You are a being made of pure energy," He noted, then he gave a nasty smirk, "However, your mind is far more malleable."

The fox gave the most violent shriek it could as The First One invaded its mind and set it ablaze, until it collapsed in the water, still alive, but undeniably braindead.

The boy gasped and fell back as The First One returned to his own body.

"What…what did you do to Kurama!?" He demanded.

"Do not be so concerned with what I have do to that beast…." The First One chided before blasting the blonde into unconsciousness. "Rather, be afraid of what I shall do to you."

He folded his arms as his machines took the boy back to the Spire for experimentation, The First One stared at the ruins of what was once the great Hidden Leaf Village, now united as ashes with the rest of its bygone era.

Gone was shinobi and assassinations, now was the era of cleansing and rebirth under his rule.

* * *

 _As it turned out, the boy's blood held the secrets for long life, and with that, I did indeed become a true immortal. What of the shinobi you ask? Dead, and their way of life has vanished from history, leaving their only evidence of even existing in my labs._

 _Despite achieving my dream of becoming a true immortal, I continued my studies on that boy, to discover how he had posed so great a threat to me, just what made him so powerful._

 _I learned much from that boy, but it became clear that his body quickly could not take much more of my experimentation, so I made the choice to dispose of him, thus truly destroying the shinobi race forever, but not before taking a DNA sample._

 _From this sample, I began to clone another one of that boy. I did not fear if he would somehow retain his memories and attack me, I had defeated him before, and this time, I had the abilities of his entire race in my arsenal, he would be far from a threat._

 _To prove my point, I even gave him his braindead pet to draw power from._

 _Why tell you this? Because this medical lab happens to contain that clone. I do not know how far along he would be in the cloning process, but it is important that you install the command modulator before he reaches the child stage or his brain will grow more resistant to our commands later on as he grows._

 _Besides this, I am quite certain that others of his village had escaped, but they are no doubt too paralyzed in fear to pose a threat against me._

 _As for the shinobi samples, they are-REST OF THE FILE CORRUPTED._

* * *

A lone man silently ingested all that was told to him. He had witnessed the genocide of mutants a thousand years ago before his very eyes, and it made him sick to his stomach.

It appeared that this….First One was eventually stopped by who knows what and who knows how many years after that massacre, but the First One had counted on that and hid much of his research across the earth for the event of his return.

Who really knew how much of his work was discovered throughout the centuries or if it still laid under the feet of humanity.

"Charles, did you find anything?" The voice of a Scottish woman squawked into the radio that belonged to the disabled man who happened to be one of the most brilliant men when it came to genetics and mutations, also a mutant himself.

"Yes Moira, I found something. Too much of something." Charles Xavier muttered as he looked around ruins of advanced technology that was used for the barbarism of one insane mutant.

Then he stared at the vat, the vat that held a young spiky haired child in a stasis, a stasis no doubt enacted when the computers recognized its power failure.

"Moira, come down here. I'll need your help with something."

* * *

 **Chapter Completed!**

 **What a way to start off a new series, with the destruction of the known shinobi world! Do you all know who did it? It should probably be pretty obvious to those who are X-Men nerds like myself.**

 **If you guys felt like that guy was too overpowered (since he took down Six Paths Mode Naruto) then I did my job right. He's supposed to be one of the strongest mutants in existence and he's backed by the advanced technology of aliens (you wanna know how advanced? During modern Xmen, it's still advanced.)**

 **Just a heads up, I'm gonna be spreadin' out my X-men wings and I won't be limited to X-men Evolution series, I just needed a starting point.**

 **That means Savage Lands! Shi'ar Empire, and I'm not spoiling anything else!**

 **Send lot of reviews and feel free to express what you thought about my first chapter.**

 **MAY THE FLAMES OF YOUTH BE WITH YOU, ALWAYS –Jedi Master Maito "Might" Guy**


	2. Chapter 2: Emergence

**I'm back! The Phantom Penance has returned!**

 **Normally, I'd be doing my other fanfics, but I'm having some slight problems with them, so I'm working on this until they get sorted out.**

 **Anyway, I have a new poll on m** **y profile, you should check it out because I plan to do some major crossover with my other story.**

 **Back to the Second Evolution!**

* * *

 **Chapter 2: Emergence**

"I'm bored! This is boring! You're boring me! Stop being boring!"

Xavier was very lucky that he doesn't have much work to do in his life, otherwise, he wouldn't have any privacy to do it.

When Naruto had matured to the good old age of twelve, his energy was at an all-time high, with no signs of stopping whatsoever. Moira was happy enough to tell him that it had nothing to do with his mutations or…..the experiments, but rather that he was just energetic.

Speaking of which, little boy Naruto had unknowingly became the gap between Charles and Moira. Xavier couldn't bear to tell her what exactly Naruto was, only that he was basically a guinea pig for one demented mutant, and the Scottish stuck to him like glue.

She spent many years observing young Naruto and playing with him most of the time, it came to the point where she built a facility not far from Xavier's mansion so that she could stay for two weeks before returning to her Medical Center on Muir Island.

"Hey! You're doing that thing where you pretend that I'm not here again! Stop doing that!" Naturally, Naruto's shouts had dragged the tortured man out from his personal thoughts.

"Now Naruto, you promised me that you would be quiet until I finished my work," Xavier chided. "It is a bad habit to go back on your promises."

The little boy with a bush for hair scratched that hair in embarrassment. "I wasn't lying, I just didn't know that you would have this much to do, ya know. I don't remember you being this boring, that's all."

Again with him being boring. Charles was _not_ boring, he just had to do things that were expected from an adult, but sadly, that concept was beyond the blonde.

Pausing from his work, the paralyzed man looked down to Naruto and his pouting face. Simply put, the child looked adorable, even to the standards of a man. His blonde hair was bush and uncontrollable and after the deaths of several razors, Xavier doubted it could ever be controlled. His eyes were huge, any bigger, and they would take up most of his face.

Sadly, that was the only part of the boy that resembled human. The rest would be considered unnatural by the laws of science.

His irises were orange with a long, diagonal rectangle for a pupil. Outside of his eyes was a red-orange tint in the space between his eyes and his eyebrows and right beside his mouth was three whiskers, but they held a close resemblance with scars.

After taking in his features, Xavier sighed at the misfortune that the boy in front of him was indeed Naruto and not some android. Androids would definitely be more quiet.

"Fine then, I can finish this later. Let's head to the sub-basement." Xavier rolled his wheelchair away from his desk as he spoke.

"Yay! I'll race ya down there!" Naruto cheered as he ran to the door. Charles widened his eyes, the boy was moving so fast, meaning he was excited, and careless….

"Don't-!" His warning was too late, for both were now staring at the doorknob and some of the door that now laid in Naruto's hand.

The boy chuckled weakly as his face began to turn red. "S-Sorry about that, Old Man X."

Professor Charles sighed once more, "Never mind, I'll replace it. Be more careful for now on."

It was a matter of time before Xavier found out the hard way what Naruto's mutant abilities were. Other than the physical attributes, Naruto was mutated to be physically far more enhanced than any human alive, even the old war hero, Captain America.

He was stronger, faster, far more durable, and held stamina far beyond that of any human. Moira and Xavier never tested to find the exact limitations of his mutations simply because the boy was still that, a boy.

There was also several other things about Naruto that made him extraordinary in the standards of mutants. Naruto had a greatly enhanced sense of perception, sometimes he could see things before they happened. It gave him the edge in possible hostile situations, or even worse, getting away with stealing midnight snacks.

Naruto also processed information very easily, he could possibly learn how to drive a military vehicle if read the manual, making it a mystery to Charles why the boy hates learning anything at all.

However, the greatest part about Naruto is that he could basically absorb any and every type of energy in existence as well as sense who was human and who was a mutant, much like to Xavier's Cerebro program.

They don't know how the boy does it and they may never find the answers unless they run into The First One again and the possibility of that happening was astronomically low **(heheheh)**. Moira was able to draw a theory about the boy's powers that the energy he absorbed could possibly boost Naruto's enhanced abilities to a higher rate, and since there was no discovered limit to his absorbing abilities, there could be no limit to Naruto's power.

Of course, it was all speculation. The adults were very wary of doing any legitimate tests on Naruto in fear that it could trigger some sort of memory of the experimentation The First One had performed much earlier in his life, the odds of that monster using any type of anesthetic on the boy was very low.

Despite that, Naruto was classed, in theory, a possible Omega Level mutant by the Mutant Power Level Classification. **(AN: I never get why they called it that, Mutant Power Level. What is this, Dragonball Z?)**

This information ran through Xavier's mind on the long elevator ride down to the sub-basement. _'Eleven years old, and already possibly Omega Level. Naruto, you were indeed made for a purpose.'_

By luck alone, the boy may never find out what purpose was his creation. Nevertheless, Xavier swore an oath the moment the boy opened his eyes that what was intended for evil, he would turn it around for good, for the well-being of Naruto, and the well-being of suffering mutants everywhere.

"Elevator's so slow! You need to make it faster." Naruto whined once they finally reached the familiar grey corridors of the sub-basement.

Charles smiled at the blonde boy, "Perhaps I was working on that upstairs before you interrupted me."

"Nah, you were working on banking and stuff, I read the notes while you weren't looking." Naruto replied with a smirk, the boy always felt pride when he accomplished things silently.

"Ah, but what if I was checking if I had enough money to make improvements?" The bald man replied, Naruto scoffed at that.

"Yeah right. We're living in a big house, like you have money issues or somethin'."

"You shouldn't make assumptions if you are watching someone," Xavier taught, "you should always make sure, otherwise, why bother being there?"

Naruto stared straight at the telepath, "What are you, some type of spy?"

Xavier stare back at the boy and gave a simple smirk, "Perhaps."

With that, the man bound to the wheel chair rolled into the booth, leaving the blonde with his mouth agape.

 **(AN: I don't remember Prof. X being a spy, however, he was in World War 2, so he does know some stuff)**

* * *

Charles calls it the Training and Exam Room, Naruto prefers to call it the Danger Room. Xavier has tried to tell the boy that the word "danger" is misleading from the training room's real purpose, but the boy doesn't care.

As always, Xavier starts off with something easy: a simple automaton that has slow movement and could barely hit a tree, and as always, that leaves Naruto a bit disappointed and the poor android is laid ruined in a corner.

"C'mon, gimme something harder! I can take it!" Naruto yelled in encouragement.

" _Or your ligaments will tear and you will have horrible muscle generation for the rest of your life, I personally prefer playing things safe if you don't mind."_ Xavier's voice came through the microphones.

Naruto stuck his tongue out at the direction of the Danger Room booth, "Every party needs a pooper!"

" _If you insist. Now, let's see how you fair against a wall?"_ Slowly, a large wall made of pure bricks rose from the ground to challenge Naruto, in his bored state.

The boy then grinned wickedly while he placed a fist into his opposite hand. "This is a piece of cake! One demolished wall coming right up!"

He placed his hands together and closed his eyes tight, showing that he was concentrating on something. He opened his hands to reveal an orb, a blue orb that was seemingly made out of blue wind, and it was moving very violently.

"HIIYAH!" The blonde boy yelled as he forced orb onto the wall. The effect was instantaneous, by that, the wall never stood a chance. Somehow the orb tore right through the brick wall with the force of a miniature hurricane.

Naruto stood proudly over the deceased wall, doomed to be a wall no longer.

"C'mon! If you keep giving me nothing but giant robots and walls to hit, I'm gonna wipe out their entire race at the end of this!" He complained as he sat down amongst the rubble.

Xavier smiled at the progress he was showing. It took him far less time to summon the power for his wind attack, and the orb alone was already strong enough to take down bricks.

' _Perhaps when he's older, he could be strong enough to shred titanium.'_ The Professor briefly thought.

"Yes Naruto...perhaps it is time-"

Whatever the Professor was going to say, it was never said as a red light flashed on the main computer. It was nothing too serious, all it told him was that Xavier Mansion was having a guest, but Xavier doesn't get that many guests. So there was the question: Who was the visitor?

Human…..or mutant?

* * *

The man's name was Fred Duncan, he was an FBI agent following a very peculiar case up in Nebraska. Recently, there was a string of robberies happening in the town of Omaha with the robber having a tendency to make a man-sized hole in the wall for an escape route.

Criminal's name was Jack Winters, and some well-placed cameras had showed Duncan how Winters escaped captivity: his hands were made out of a hard substance, most likely diamonds.

Very few people in the police force know what's going on because of a department in the government has been keeping things under wraps. All Duncan knows is that every potential domestic threat to the country is being monitored by them, and the agent was wise enough to know that is information should end there.

Things could have been handled smoothly by the FBI when all the sudden, Winters changed course in his robbing spree. He went from small time jewelry stores to raiding scientific labs, and he wasn't doing it alone.

He had somebody with him, somebody small because he was always just out camera's sight, but this small person could unleash red beams of destructive power, and he helped Jack Winters steal precious isotopes.

Duncan's hands were tied, there was no one he could depend on that could somehow help him with his predicament, so he went to the well-known Professor who talked about evolution: Professor X.

Xavier briefly used Cerebro to confirm that Winters was no mutant, but his friend was. Dwelling deeper, Charles also found out that his friend was indeed a boy by the name of Scott Summers. He was a runaway from an orphanage and separated from his other brother who was quickly adopted by another family.

Charles knew that Summers was exactly the type of mutant he wanted to help in his budding Institute, so he "asked" Duncan to take him along to Nebraska with hopes that he could reach the Summers boy first before the police or his orphanage, if they even care.

However, after calling Moira to watch over Naruto in his absence, followed by someone sneaking into his luggage, Charles had no choice but to bring Naruto along.

"-as long as you stay right next to me-"

"What's this do?" In a flash, the boy was already messing with one of the radios the FBI were using, Xavier could only sigh. It didn't matter much, as long as Naruto was in sight range and _well_ within telepathy range, he should be alright.

"Hey Prof, come take a look at this," Agent Duncan called out. The man bound to the wheelchair took a pair of binoculars and scanned an abandoned lab facility.

"Our boy's holed up in there. However, this is a highly respected lab, no telling what built-in defenses it could have." Duncan said.

"Then you should tell your men to exercise caution," Xavier replied, "especially around the boy, he could be-"

"Sir!" Both men (and child) turned around to see a SWAT officer behind them, and in his hands, a phone.

"Phone for you. It's urgent." The FBI agent, albeit a little confused, took the phone and headed off to the side.

"Hello, who's...yes, I'm the man in charge. Pull-sir, do you have any…yes, I know who you answer to. Right away." Duncan hung up and returned to Xavier, he looked especially madder than normal.

"New orders, we're pulling out." The FBI agent barked,

"What?" Xavier gasped, "Mr. Duncan, we simply cannot stop here, a boy's life could be a stake!"

"I know Prof, but it's not my call." Duncan replied apologetically, "Some department from the higher up apparently has some dealings with this facility, so they want to handle Winters themselves. I can't believe they called the friggin' President to get permission."

Now, it would be so easy for Professor Xavier to tell the men to proceed as planned, but they would in turn lose their jobs, or worse, sent to jail for insubordination.

All Xavier could hope for was that whoever was in charge would have the decency to leave Summers out of this mess-

"Hey, where'd your kid go?"

* * *

After Naruto had heard that the FBI was running away, he decided it was time to take matters in his own hands. This kid was going to be his first new friend that was his age, and no cowards was gonna stand in his way from making friends!

Easy way would be to take the halls, but Naruto was a super spy, and like any other super spy, he took the vents.

' _Naruto, turn back around this instant'_ a voice penetrated his mind, and it wasn't his own.

' _Sheesh, 'bout time you showed up. It was getting boring being alone,'_ Came the reply of the blonde.

' _I am serious. This man has mental abilities as well as I. I won't be able to stop him should he attack you.'_ Xavier replied in the most serious tone he could muster.

' _Heh, I'm not scared. I can beat him down, no problem!'_ The boy mentally boasted.

' _You destroyed a brick wall, Naruto. Brick and diamond are two different substances altogether.'_ The bald Professor replied.

' _Yeah, sure. Just wait, you'll be amazed by my awesomeness! Later!'_

' _Naru-'_

And just like that, the Professor's voice was gone. It was never explained, but if Naruto really wanted to, he could kick the Professor out of his mind, but first, he'd have to be aware that Xavier was in his mind in the first place.

Anyway, the boy reached the end of vent, so he kicked a hole in the bottom, and landed right in front of an elevator.

He pressed the down bottom a few times, but nothing had happened.

"Power must be out or something," He mumbled before grinning, "Guess I'm gonna have to do it the hard way!"

His hand was like a hot knife, and the elevator doors, smooth butter. With barely any effort at all, he wrenched the two doors wide open to reveal the long and dark elevator shaft.

"Long way down," The boy muttered before looking to his left, "Alright, some ladders! If I fell, I probably would've gone 'squish!'"

Even though he was safe enough on a ladder, the ladders could not protect him from a fear of heights and an over-imaginative brain. Little by little, step by step, the bushy haired boy descended the ladder until his feet landed safely on the top of the elevator.

His hand smashed through the top of the elevator, allowing him to fall through and force it open. Naruto walked down the abandoned hallways, briefly noting the destruction of several rooms containing all sorts of science stuff.

"-you mess it up, I'm gonna fix your face. Permanently!"

Naruto snapped at attention when he heard the gruff voice of a full grown man at the end of the hall. He ran down that hall and crept right at the wall, then peeked at the edge of the wall to see the bad man Professor X was talking about.

He was bulky and had short, brown hair, but his face looked like it was permanently seared as a scowl, but the weirdest thing about him was that he was strapped to a chair with a giant gun pointed at his face.

The blonde boy scanned the room a little more to find the boy. He was a mess, wore rags and he had bruises and injuries just about everywhere, also he wore a pair of glasses that had a deep red color. The kid was the one managing the gun that pointed at the bad man.

"Well, whadd'ya waitin' for!? Turn it on now!?" The man barked. The boy cowered for a split-second before turning on the machine.

Naruto recognized the hum of the machine, indicating that it was powering up and about to fire, then it did fire. Green beams of light struck the man straight in the chest. He yelled in pain as the light became unbearable to witness by the human eye, so he turned away till the light dimmed.

The man slumped back into his chair, then he flexed his arms, finding new strength in them.

"Power…." the man gasped before starting to laugh maniacally.

"Raw Power!" He ripped through his restraints as his entire body became pure white, like a diamond.

"I'M INVINCIBLE! UNSTOPPABLE!" The man raved as he buried his hand within a wall.

"M-Mr. Winters," the boy began feebly, "Y-you promised that if I'd help you, you'd let me go."

The man stared down at the boy behind the glasses.

"Yeah….I said somethin' like that, didn't I?"

The boy cried out as the metal man lifted him up by his shirt. Naruto growled at the notion that the metal man was enjoying the boy's despair.

"Well, Summers, that was before you helped me. Now that I'm unstoppable, you're gonna learn to take orders from me, just like the rest of the world. They're all gonna learn to listen to the Living Diamond!"

He tossed the boy to the ground and continued his laughter, the boy stared at him in fear, but soon, they were gonna find out that Jack Winters wasn't laughing alone.

"I get it! The Living Diamond!? That sounds like the stupidest thing I ever heard!"

"Who's out there!? Show your face you punk!" The Living Diamond commanded.

"I'm down here, idiot."

The man looked down to see a little kid. He stared for the briefest of moments, then he laughed.

"A kid!? What do you want, you little runt? A candy bar?" Winters laughed, though secretly, the kid's unnatural eyes was kind of creeping him out.

"My name is Naruto! Remember it, cuz it's the name of the kid who's gonna beat your face into the pavement!" Naruto boldly declared, making Winters laugh even more.

"Runt, lemme tell ya, you got a promising career as a comedian! Or at least, you will if you go back the way ya came and never come back."

Winters made a move to shove the boy around, but the boy grasped his diamond hand and squeezed, _hard._ Before the Living Diamond could protest, Naruto lifted the man over his shoulders and threw him through a few walls, and possibly the elevator.

The Summers boy could only gasp at the apparent strength the blond possessed. Suddenly, the blonde haired boy turned and faced him.

"Hey! My name's Naruto! What's yours?"

* * *

"-So you see, Scott, my Institute is made to help people like ourselves, mutants." Professor Xavier concluded after Winters was apprehended and Scott was treated for his injuries.

The Department that owned the science facility had sent two particular agents to deal with the problem. Naruto laughed at their surprise that a mere child handled their problem, though Naruto was excited to find out that the agents were also super-spies "like himself."

They were rightfully suspicious that an eleven-year-old took down a meta-human by himself, so Xavier could expect that this….SHIELD would be watching over him from now on.

Despite that, if Naruto's story about the Living Diamond showing pain when he grabbed his arm, Charles was astonished that the boy's strength already had some affects against diamonds.

Off-topic, Summers was naturally reluctant to join Xavier, he feared that he may be placed in another orphanage and he still wanted his brother. As painful as it was, Xavier had to stress to the boy that his brother Alex could be living with a family that loves him and that it would be selfish to rip them apart.

"Can we at least try to find him?" The boy pleaded.

"I don't see why we shouldn't." Xavier smiled before he felt a vibration in his pocket. He pulled out his cellphone.

"Charles Xavier here."

"Are ya finished with your business in Nebraska, by any chance?" Xavier instantly recognized Moira's voice.

"Yes, we are done here."

"Good, because your friends called from New York. She's done it again, it seems."

Xavier narrowed his eyes in concern. There was only one person that lived in New York City, outside of Moira, who knew what Charles Xavier really was. If Moira was talking about the same person he was thinking, then it was finally time.

It seems he, Naruto, and Scott would be taking a slight detour from the Institute.

* * *

"Professor, what are we doing here?"

"Yeah, what are we doing here, old man?"

Charles didn't tell Scott and Naruto the purpose for driving to an average neighborhood because he wanted to keep it a surprise for the boys, but Naruto was quite insistent on finding out the whole plane ride back to New York.

"You see, I had found another mutant a few years back and under the request of her parents, I had given her private lessons to control her power." The man replied at the doorstep of a yellow house.

Naruto gasped, "Well, why didn't you tell me? Or at least bring her to the mansion?"

"Her parents felt that was too drastic of actions, but that may have to happen at this point." He replied.

"Why? What happened?" Scott asked with concern.

"Nothing serious." Charles reassured as he rang the doorbell. Naruto glanced at the mailbox in front of the house. On it, in red paint, spelled the word "Greys."

"That's a cool last name," Scott said. Naruto lowered his head at the mailbox.

"Wish I had a last name," he muttered, confusing the boy wearing shades, but that topic wasn't discussed upon for the front door was opened.

"Good morning, John, or is it afternoon now?" The Professor greeted. Naruto looked at John Grey, he had brown hair that was just getting grey hairs in it, and his face looked like he had a nightmare, or was living in a nightmare.

"Oh thank goodness, you're here. She's been in her room all day." He spoke quickly and invited the bald man in, though he paused when he saw the other two children.

"That is Naruto, the boy I told you about, and this is Scott, he's quite new to my Institute." Xavier supplied.

John Grey smiled briefly at the two boys, "Scott and Naruto eh? My daughter loves to make new friends, I'm sure she'll like you."

"Well, I like her already! Let's see her!" Naruto exclaimed with his old enthusiasm returning. Xavier smirked at the declaration of the blonde boy, he knew Naruto didn't know that his reply could have been taken wrongly.

"Sure, if she'll just leave her room….." John muttered as the four of them all migrated to the living room where a woman with short brown hair awaited them.

"Hello, Elaine. You look as stunning as ever." Xavier shook the Mrs. Grey's hand, but she looked just like her husband: scared beyond belief.

"It's good that you came Professor. After….the incident, she wouldn't leave her room for anything. Food, friends, school, and you know how much she loves school…"

"Why don't you tell her I'm down here, and we'll sort everything out." Xavier assured, breaking through the woman's rambling.

"Y-yeah, yeah! That'll work…" Both of the Grey's nodded and left together up a flight of stairs.

"Geez, what's got them acting like jello?" Naruto snorted.

"Jello?" Scott questioned.

"Ya know, all fidgety and stuff." Naruto explained, earning an 'oh' from Summers.

"Forgive me, but John and Elaine's daughter is a rare type of mutant. She can read minds like me and move objects with her mind." Professor Xavier explained.

"Now a mutant like that is very rare, very powerful. Powerful enough that she could read the thoughts of everyone around her with ease, and I personally know how nerve-wracking that can be."

' _Also, there is the matter of how she awakened her abilities, amongst other things.'_ He privately thought, for those were a subject that the young Miss Grey should herself.

Speaking of which, the three men all sat up when they heard the Greys go down the stairs.

"Well, Naruto and Scott, meet our daughter, Jean."

Naruto had not seen a girl his entire life, and Moira MacTaggart was technically a woman, so she didn't count. However, he'd still safely say that Jean Grey was without a doubt one of the most beautiful women he had ever seen, and judging by Scott's similar reaction, he wasn't wrong.

Perfection laid in the simple things, and Jean was the epitome of simple. She had long, simple red hair, simple eyes, a simple, and unblemished, face.

The day will come when puberty sets in, and her womanly attributes will start to take form, but as of now, she was simple and that was beautiful. Natural beauty.

Other good news: Naruto's a poet deep down.

"You're perfect."

Annnnddd, he totally made the moment incredibly awkward. Nice going.

"My, t-that's quite forward of you, young man," Elaine Grey stammered in embarrassment for her daughter who was also beet red.

"Yes, I'm afraid Naruto here is well known for that," Xavier chuckled, "but that is his strong suit in many instances."

Naruto laughed while scratching the back of his head, "Y-Yeah, silly me…..but I'm not taking it back!"

"And it would be quite rude if you did." John Grey added while smiling at the boy, relieving Naruto of his tension.

"Why don't the kids play outside while we talked?" Elaine suggested, Naruto bobbed his head quickly at the thought.

"Yeah! I can tell her my awesome story of saving Scott's butt!" Before anyone could refuse, the blonde dragged the brunet and the red-head outside into the backyard.

"You said he was hyperactive, but I didn't believe he would be this hyperactive," John Grey chuckled, but then he sighed in depression.

"Then again, I didn't believe a lot of things you told me."

"It was so bad this time. The whole house shook," Elaine explained. Once they all sat down, she proceeded to tell Professor Xavier how Jean nearly destroyed the house while she was having a nightmare.

"It was about Annie again, wasn't it?" Xavier asked gently, poor Annie was as much a scar to the parents as it was to their daughter.

"It was careless of me, I didn't watch her. How could I, her own father, let my daughter cradle her dying best friend?" John grieved lowly.

"That was not your fault, John. Your daughter does not blame you for that accident," Charles comforted, but the man only stared at the ground.

"But I get the feeling that she doesn't forgive me either." He only muttered.

"Is she going to be alright?" Mrs. Grey asked with concern.

The Professor narrowed his eyes in great thought. "I'm not certain any more. This….power inside of her, I am positive that it is trying to break free from her hold by haunting her in her dreams. I feel that with her minimal level of training, it will be free soon enough."

Of course, the couple caught on quickly what the paralyzed mutant was suggesting.

"You want to send her to your Institute, don't you?"

"It may be the best option for her. If she goes there, I can know how she is doing and have more than enough time to train her how to use her abilities." He urged.

"But of course, it is, above all, her choice if she wants to go or not. I can always just have longer and more frequent lessons from here."

Wife looked hesitantly at the husband who returned the look, then sighed.

"Jean….wants to go to the Institute." He admitted. "She told us one night. Told us that she didn't trust herself anymore, that she needed more."

He looked up and out the back window, and started to smile again, "I think…she might like it there. Your kid sure can make her laugh."

Xavier looked outside to see Naruto, grinning brightly at his triumph of making both Scott and Jean laugh, or at least, he assumed they were laughing since all he could see was the two shaking.

Then, he finally caught what John was saying.

"What? Oh no! Naruto isn't my son." Charles rejected quickly, confusing the Greys.

"Really? But you spoke of him so fondly, and he clings to you like a son would do to his father."

"I do entertain the thought, but Naruto isn't my child. That is behind me." Xavier reassured although his own answer was bringing a frown on his face.

There was very much doubt on the faces of Jean's parents, but it was far from their concern now. What was their concern was the well-being of their daughter.

John Grey shrugged at his wife as he spoke. "Well, if there isn't any problems, I guess we'll get Jean packed, then tell her the news. I assume we can visit."

"Anytime you feel like," Xavier assured. His dream of an Institute for mutants was slowly becoming a reality.

* * *

"It's so huge!" _Both_ Jean and Scott exclaimed at the front entrance of the Xavier Institute for Gifted Children. Naruto only laughed at them.

"Just wait till you see your rooms! We can all have rooms right next to each other, or we could just sleep together, whatever you guys want!"

It was very clear that the blonde was having the time of his life. He expected only one new friend, but to his surprise, he got two! Now he could play some group games and stop having to depend on X doing his boring work.

Charles was smiling at the enthusiasm of his new students. He could tell that they were going to be the trailblazers of a new path for the world, a path that will be traveled by mutants and humans, coexisting to find peace.

Suddenly, his phone vibrated once more. He checked the caller to find it was, once again, Moira.

"Yes Moira, how can I help you?"

"More like how can ah help you, Charles." She joked, most unusual for her.

"Anyway, ah found two mutants for ya. One you already know, the other, very two. Ah'll send you their location."

"Thank you, Moira." Charles replied before she hung up. His phone received the coordinates, Xavier frowned at the distance of one from another, but oh well, Rome wasn't built in a day.

Next stop: Canada, followed by Africa.

 **Chapter Two Completed!**

 **Now that was a lot of words and a lot of work! Got a couple of things I need to work out first. Naruto's skirmish with the Living Diamond was short for a reason, and not because I got impatient, but he was literally a minor villain in the X-men. Like really minor.**

 **Anyway, for all you wanting to know the pairing, it isn't straight NarutoxJean. That's not how it works in the Marvel Universe. There won't be a straight paring because this is X-Men, and stuff goes DOWN in X-Men.**

 **People DIE in X-Men…..actually, people DIE in Marvel in general.**

 **Anyway, when the going gets tough, Naruto's gonna roll with the punches, and the kisses.**

 **Other matters, his powers. Basically he's stuck on Sage Mode for the rest of his life, and to sweeten the deal, he can possibly absorb as much energy as he wants and that energy strengthens his body, making him nearly unstoppable.**

 **I'm saying nearly because his battle with Apocalypse is gonna be edgy, I'm debating if he should lose any limbs or eyes.**

 **MOST IMPORTANT PART: SEND ME QUESTIONS, COMPLAINTS, ANYTHING, AND I WILL ANSWER THEM IN THE NEXT CHAPTER. I'M TRYING TO BE COOL LIKE THAT.**

 **AND NOW, FOR THE MOST IMPORTANT PART OF THEM ALL:**

 **MAY THE FLAMES OF YOUTH BE WITH YOU, ALWAYS**


	3. Chapter 3: Emergence Pt II

**What's up my fellow people! The Phantom Penance has made a comeback!**

 **It's been some time, the answer to that question is that I've been traveling and I had my fair share of summer camps, but for the whole month of July, I'm back.**

 **Before the story begins, I promised that I would answer some questions, and I will. STARTING NOW**

 **Q & A TIME:**

 _ **Keyblade Master Cole:**_ **Naruto will stay the same, that's a given, and he might have to kill Apocalypse because I intend to make the fight desperate (for Naruto, at least)**

 _ **Spark681:**_ **I can't promise that because I have an internal struggle deciding if Kurama should stay comatose or not, I'm leaning on not for the moment.**

 _ **Potterfanforever:**_ **Naruto having memories of his clone donor (that sounds weird) is a little etchy. It's possible…**

 _ **Mecaldar:**_ **I never said that the shinobi race was dead, I said that Professor X** _ **thinks**_ **they're dead. However, their way of life is undoubtedly dead since chakra would seem like a fairytale to their children and their children's children and so forth. There were survivors, but in the present day, there are no more shinobi.**

 _ **Vatsyayana69:**_ **Apocalypse is an Omega Class mutant with the technology of aliens known as CELESTIALS at his beck and call. I know this seems kind of silly, but Mecha Naruto was able to take care of Kakashi, Naruto, Yamato, Kiba, and Neji just fine. I may have missed one other character, but shinobi and their chakra never faced technology lightyears beyond their own.**

 _ **Grimreaper 40045:**_ **I'm gonna be honest….I may have forgotten the truthseeking balls a tad bit. But in any case, they could destroy anything, but they would have to go through Apocalypse shields first, and if Apocalypse was smart, he'd have a self-repairing shield. It's like I said, Celestial technology is far more advanced than any shinobi has ever dealt with.**

 **That's all the questions I think! If you don't like the answers, just remember that I am human and definitely not the owner of Naruto, I can make as much mistakes as the next guy.**

 **Anyway, now that the introductions are behind us, let's get on with the story!**

* * *

 **Chapter 3: Emergence Part II**

" _ **STOP LAUGHING!"**_

The whole house shook and shuddered by pure power and all the rage a child could muster.

Magnus, or Erik to a few, was already on his feet the minute he felt the small quake, he was well out of his study and heading down a wooden hall to a very special room: his children's room. Before he got close, there was a blur and his son appeared before him.

"It was my fault, really! I started it!" He said quickly, trying to dissuade his father from the real culprit of the tremor

"Move Pietro." Was all Erik said before he pushed his son out of his way to the room. When he opened the door, he was greeted to a sight of carnage, clothes were all over the floor, furniture was ripped apart, and in the middle of the carnage was little girl with short, brown hair.

"Wanda, what have I said about using your abilities!?" Erik demanded.

The girl sniffed, "I….know, but Pietro was being mean to me!"

"And you deemed it fitting to destroy your room because of your brother?" Erik questioned his daughter. She only looked downward in shame.

"I'm…sorry." She mumbled.

The elder man merely sighed, "Apologies can only go so far Wanda, and an apology cannot fix your room."

He knelt down to his daughter and placed his hand on her shoulder, the closest thing he's had to affection for his children.

"I am proud of you and Pietro, you have both unlocked your mutant abilities far sooner than I did, but now I see that is a mistake. You lack the will to control your powers and teaching…is a skill my friend has learned instead of me."

"Something will have to change. You cannot keep destroying things in a mixture of emotions and I cannot teach you. There's only one option…."

* * *

No sooner did the trio enter the mansion that was to be their new home, they were carted off again on a new trip, not that Naruto minded at all. New places, new faces.

This time, they went up North from the cold North of the Americas to the moreso cold land of Canada **(I like to call it Canadia).**

As it turned out, the trip was only to be in vain.

Despite all the trouble Charles and the children took to reach Canada then go up the mountain that made the home of the mutant, said mutant was still uninterested.

Not much was known about the man, except that his name was Logan and he had an incorrigible drinking and smoking habit. His sideburns looked cool to Naruto, and to the displeasure of the man, the blonde boy couldn't leave the Canadian alone for a second, though his demeanor scared Jean and Scott off.

Logan possessed unique abilities that revealed that like Naruto, he too was experimented on, but he did not know who did the experiments and for what purpose since it rendered him an amnesiac.

Despite that, Xavier could tell straight off the man was a soldier at heart and his dogtags he fondly held onto confirmed that much. The last time Xavier found Logan, he was serving a top secret branch of the Canadian government that handled certain missions that were deemed to be suicide for normal people.

Logan admitted that he came back from one very recently. He didn't say much, only that he had to deal with something big, green, and had a temper that matched his own. Circumstances arose that compelled him to pull out before completing his mission, and that was when he decided that he was done killing people and went AWOL on the Canadian government.

Speaking of circumstances, a nasty blizzard had forced the four New Yorkers to hunker down with the man for the night, Charles thought that it was happenstance, but Logan blamed it on someone called Shaman.

"Coverin' their tracks so they can find me. No one runs off on Alpha Flight _or_ Department H. Hn, lucky that I did both." That was all he would admit.

Nevertheless, that gave Xavier a whole night to convince Logan to come with him as well as handle Jean's problem as well. Scott would sadly have to wait when they were safely back in New York or perhaps even Africa. If he opened his eyes without the safety of the ruby quartz glasses, Logan's entire house could suffer for it.

He expected Naruto to behave himself, technically, he did. It's just that no one could have possibly foreseen what was going to happen when Logan stepped out to meditate and the blonde followed him

Wolverine sat in the middle of a small room with no shirt to cover his very hairy chest. It was funny how he still called himself Wolverine, he guessed that name described who he really was, a feral animal. Amnesia meant nothing, the rage, the bloodlust, it was all genuine.

But right now, the Wolverine had to rest, to become one with all of his senses, and meditate on his memories. Meditating on the memories was far better than having them as nightmares, his body was calm and prepared for any….discomfort in meditation mode and when he wanted to sleep, his body craved nothing more than to rest until the memories attack him.

Japanese traditions would dictate that he lit incense, but the aroma usually would throw his heightened sense of smell in a loop, so he'd had to do without.

' _Nuff distractions,'_ his consciousness scolded to end the thoughts that plagued his mind, _'Time to med-'_

"Hey fuzzy man, what'cha doing?"

To Logan's extreme luck, the runt had decided to show.

"Mindin' my own business. I suggest you do the same." The nigh-feral man growled to the kid with a bush for hair.

Naruto stared with eyes full of curiosity at the pose Logan was doing, he had never seen anything like it before.

"You're sitting down and your eyes are closed, are you trying to go to sleep or something? Cuz that's a terrible way to sleep, doesn't look comfortable at all."

Wolverine fought down the instinct to eviscerate, tear something apart. "I'm meditating. It's this thing we grownups do to ward away annoying little gnomes, and it's clear I ain't meditating hard enough."

It was so clearly a jab at him, but unfortunately for the small man, that only made Naruto more interested.

"Hey, fuzzy guy! Teach me how to meditate! There's gotta be more to it than that! C'mon, show me please? Please? Pleasepleasepleasepleaseplease-"

' _It…..won't….shut up!"_ Logan's mind raved with agony over the continuous annoyance and there was no end in sight with the whammering.

"Allright…Fine!" He snapped. "Get in a position, like me."

Naruto smirked with excitement and did as he was told. He sat down with his legs criss-crossed and placed his hands between his legs before he frowned.

"This feels off, can I do this instead?" He asked as he connected his two fists by the knuckles.

"Sure, whatever makes ya' feel happy, and shuts you up," Logan dismissed, though he said that last bit mostly to himself.

"Now, the most important part is that you DON'T MOVE and that you DON'T SPEAK. Got it?"

Naruto pursed his lips, "Don't move, don't speak. Are you sure?"

"Ain't never been more positive about anything in my life," Logan grunted as he closed his eyes again, "Now close yer eyes and concentrate on whatever makes you feel happy, and remember: no moving, and definitely no speaking."

"What if I have a question?" The boy asked.

"Then it sucks to be you," Logan replied before he went back to his precious meditation.

Naruto scowled at the man _'Cheeky….I'll show him!'_

Logan smirked, it seemed that the kid had finally shut himself up. He probably did old Chuck a favor, maybe he should take advantage of this wonderful opportunity…

' _What can Chuck give me for shutting the runt up? Beer? Too easy. A new bike? I did have my eyes on a model-'_

He could have gone on and on, until he caught the scent of blood, lots of blood. Hot blood.

"What's goin' on here?" Logan growled. His hands curled into fists as three claws made of an unbreakable metal pierced his skin and rose from within his hands. His nose followed the blood's metallic scent, but it would not have to go far. He merely had to look to his side. The sight that greeted Logan was something he would not quickly forget in a long time.

"What the-"

Xavier was the first to feel the thoughts. The rage, the bloodlust, it was very potent, nearly unbearable. Jean cried out in brief agony when she quickly felt it after him while Scott just stood there, feeling helpless. But as quickly as it had arrived, it soon vanished, leaving the telepaths breathless and confused.

"P-Professor, what was that awful-"

The cabin shook violently as it was hit by what felt like an earthquake. Furniture and utensils were shaken to the ground where they fell or even shattered to pieces and the three mutants held onto something to steady themselves.

Finally, it stopped.

The rumbling only lasted for a few seconds, but it felt far longer than that to the children. Logan's house was worse than wear, but no one was hurt. At least, Jean and Scott weren't, Naruto and Logan's fate was uncertain.

"Professor, what was that!?" Scott asked in bewilderment.

"I don't know, but we must check on the other two!" Charles exclaimed, they rolled to the spare room and forced the door open. The sight that greeted them was something they did not expect at all.

Naruto was fine, completely unhurt, though his fist was outstretched and pointing at a portion of the cabin that looked like it was hit by a wrecking ball.

Outside the cabin was an earthen crater, meaning that the blonde struck something with enough force to go through timber and earth.

"What did you do Naruto?" Xavier exclaimed.

The boy faced his guardian with a surprise, he tried to form words, perhaps to make an excuse.

"…I don't know, but I do know this: It was totally Fuzzybeard's fault!"

* * *

Due to Logan's healing factor, no real damage had been done at all, minus the cabin. Logan was unhappy to say at the least and wanted Charles to compensate for his house which the Professor deemed more than appropriate, provided that the Canadian told him what happened.

Logan explained that he taught Naruto the basics of meditation to stop the boy from interrupting his meditation time. It worked, but a strange aura surrounded the boy, Logan described to be liquid-like and red, likely made out of Naruto's blood which Logan's scent caught wind of.

The man didn't know what was happening, so he opted to forcefully pulling Naruto out of his meditation via a kick to the shoulder. The boy….didn't take it kindly.

Charles had a talk with Moira to explain this phenomenon, and there were able to come up with something firm.

Xavier deduced that meditating, or rather staying still for a long period of time, was another form for Naruto's mutated cells to gather energy, but it seems this energy mixed up with something else and began to decompose Naruto to the molecular level, at least very slowly.

But this decomposition gave the boy heightened strength. Granted, he was very strong already, but he was capable of using such strengths when he was excited, when he was in a great emotional state. This time, he was calm, and he punched Logan out of cabin and 30 feet out into the snow.

' _Seems that while Naruto is also meditating, he's incredibly easy to provoke, hence the negative thoughts me and Jean felt. But, to be that fierce, that evil…this is something no boy should have. Not even Erik..'_

It was quite clear that the First One made this ability as a last option for Naruto. Should he be cornered by his enemies (whoever they could have been), the boy would call upon greater power at the expense of his own life.

Xavier stared at the blonde boy, he hadn't spoken much since they left Logan, though Jean and Scott had tried their best to cheer him up.

' _It's been two weeks, three at best, and they already treat each other like siblings,'_ Xavier thought proudly. Acceptance of fellow mutants is always the first step to acceptance of humans, now there was step 2 to 100 to go.

As quickly as the youngsters of Xavier's mansion had left Canada, they were on route to native Africa to find another mutant, though she will be even harder to convince, much harder than Logan. He was soldier, a survivor, and she is a queen. A goddess to her people.

That matter was reserved to when he finally meets her, for now, he had to handle the mounting trial of finding her. Africa was a large continent and a dangerous place for the unprepared, all Xavier could do to pinpoint the mutant was with a portable Cerebro and he had to be careful to avoid from accidentally entering a tribe's territory and endangering the children.

Much like the cold of Northern Canada, the children were having much trouble adapting to the heat with Naruto being the one to voice out how difficult it was for them.

Nevertheless, they could stay at the Mansion alone and Moira was not there all the time, so they had to come with him to Africa.

It took about three weeks, but they found the mutant in the end, and Moira was wrong. Charles had met this woman many years ago, when she was a child.

He knew her as Ororo Munroe, a small time thief in Cairo with a dreadful case of claustrophobia. Her abilities hadn't manifested back then, but he treated her to a meal out of the bottom of his heart for her plight. Somehow, she traveled South of Africa to a native tribe from where her powers to manipulate the weather manifested.

To her and Charles' surprise, the villagers treated her not like a witch, but as a goddess. She ruled them with a gentle hand until she became an adult with a goddess-like body to match her powers.

Speaking of her body, when he met her, Naruto had a few words to say to Ororo once he met her….

" _Halt! Come no further strangers!"_

 _To say that Charles and the children were ambushed would be lying, for even Jean knew they were coming many feet back. The natives surrounded their vehicle and brandished their spears and arrows at the New York mutants._

' _Stay calm Scott, Jean, Naruto.' Xavier mentally assured over the three._

' _Ne, I can take 'em, easy!" The blonde confidently replied._

' _That would eliminate our purpose of being here as non-hostiles, Naruto. Please, allow me to handle it.'_

" _We do not wish for any trouble, brave men." Charles assured as he placed his hands into the air._

" _We will decide if you are or are not trouble, outsider!" One man snarled viciously as he pointed a spear at Charles head._

 _This man was different from the rest, he had a skull painted on his face and also wore ornaments. It did not help that Charles could mentally feel the man's greed for power and bloodshed._

" _We should take the outsiders to the goddess. She'll decide what their fates shall be." One man spoke in the language the natives grew up with._

 _The skull man spat to the ground. "We are more than capable of handling this! She needs not turn her attention from the skies to these vermin."_

" _I believe I shall determine what deigns my attention, Hungan." The voice came from the sun, or rather, the person floating in the light of the sun._

 _The natives instantly dropped to their feet and bowed at the voice, though the man known as Hungan was very reluctant to fall on his knees. Down floated a woman with a rich colored brown skin and unusual white hair._

 _Once she landed in front of Charles and the others, all four of them each had a reaction to the fact that she wore nothing to hide her entire upper body._

 _Charles remained respectable and had no visible reaction, Jean blushed at the woman's impressive breast size, Scott blushed then looked away, and Naruto-_

" _AHH, MY EYES! WHAT, ARE YOU CRAZY LADY!? PUT SOMETHING ON OR YOU'LL BLIND SOMEBODY!"_

* * *

Indeed, the first hour was very hectic, but once the death threats had calmed down as well as the spears, Charles could finally tell Ororo why he had come to Africa.

She did not make a physical reaction nor could Charles pierce her thoughts, she was incredibly strong willed. She invited them back to her home for the night and commanded the natives to feed and entertain the children while she and Charles discussed the matters more privately.

"I have not forgotten you, Charles Xavier. This may not be as good as a restaurant in Cairo, but it is the best my people and I can offer." She spoke while presenting her village's delicacies.

"I thank you for your village's hospitality, Miss Munroe." He replied in respect.

"Call me Ororo, and it is the least I can do for the kindness you showed me all those years ago." Ororo replied. She and Charles were currently at the footsteps of her own temple that overlooked all the village she protected, a considered sacred place to the villagers.

"The blonde one, he is quite bold and outspeaking." Ororo commented.

Charles chuckled, "Did you perhaps notice that when he spoke, or when he was offering you his shirt to cover up?"

"Both, did you not tell him that the rules of modesty in the environment he grew up in does not apply to the rest of the world?"

"I'm quite certain I did, but he rarely listens to 'boring' things." Charles chuckled.

The two adults nodded at each other in amusement before a somber spirit had returned to the dinner.

"Charles," Ororo began. "I understand the reason why you need me to come with you to America, but it is for that same reason that I wish to stay here. I am needed here."

"I understand your reasons and respect your conviction to these people, but there are thousands upon thousands of mutants in the world, I have seen them, seen their dreams for the future, and in order for their dreams to be achieved, I need people like you to help me. People who have accepted that their mutation is apart of them."

"I have done so, yes, and I use it to help my people here. Without me, they would have suffered for many months, then died!" She insisted,

"I'm not denying that what you are doing here is not good in any form of fashion," Charles replied, "but the reason you are so successful here is because these people have accepted you as a deity. The rest of the civilized world are not as accepting. Believe me, I and several others have seen first-hand how cruel humans can be to those they deem 'inferior.'"

Ororo looked away from the man, the confliction raging through her mind was clear to Xavier, telepath or not.

"You don't have to answer immediately," he assured, "After all, I only have three students now. I just wanted to give you your options and know where I can find you when you wish to make a decision."

The goddess nodded her appreciation to Xavier before she spoke again. "I…..wish to sleep on this. We may talk again in the morning."

* * *

"NO! I DON'T WANNA GO! FATHER! DON'T LET THEM TAKE ME!"

Pietro did his best to block out his sister's screams of fear and protest, but a four-year old had no chance but to be taken away by the two orderlies of the Ravencroft Mental Institute.

The boy stared at the muddy ground of black dirt when he felt a large hand gently pat his back. He looked up to see his father, the only man Pietro held in high respect, looking down upon him with sympathy.

"Someday, you'll understand Pietro, and so shall your sister." He vowed as he stared on.

Seeing Wanda struggle so brought back the worse kind of memories in Erik, of his time when he struggled against two men pulling him away from his mother, the only difference was that the Nazi stormtroopers held far less regard to him than the orderlies do for her.

"She…..she won't stay in there forever, right?" Pietro asked with uncertainty.

"Of course she won't, I have no intention of locking any child away forever simply because they cannot control their gifts, much less any child of mine." Erik assured.

"Think of this as Wanda's test, the first of many to come. She must be strong to overcome this, for she must be strong to embrace the world I plan to bring."

Then there came another scream, but this one was different from the others. Wanda's eyes briefly flashed a crimson red as she screamed with all the power a little girl could muster. The men handling her flew back from the girl while red bolts danced around her at the doorsteps of Ravencroft.

Suddenly, an old woman stepped out of the black car that brought Wanda to Ravencroft. She stared at the little girl, the little girl stared back, and then she quickly fell asleep.

Pietro was quick to catch his sister before her head connected to the stone tiled ground.

"What did you do to her?" He exclaimed in fear.

"Do not worry Pietro," Erik walked up behind his son. "Your sister is merely asleep, this will make the process of handling Wanda smoother. Now, say your goodbyes and wait in the car."

The boy glanced back at him, then stared back at his sleeping sister before he muttered something inaudible and walked slowly back to the black car. The elderly woman joined Magneto's side and stared down at the girl.

"She hold much power and a clear affinity to the mystic arts, it will only grow stronger as she grows older. I fear that this course of action is too hasty and will lead to a precarious outcome." She stated with worry.

"You worry too much for what might happen in the future, Harkness." Magneto replied. "Once she has controlled her powers, I will determine the future of humanity and mutantkind."

Agatha Harkness continued to stare down at Wanda, her destiny was a blur to the old woman, and that was a bad omen. It meant she may bring great good to the world, or great evil. Perhaps both.

And unlike Magnus, she was not fond on gambling the future.

"I assume that these homo-sapiens will have some memory modifications as well as a little 'leash' for my daughter." Magneto spoke.

Harkness stared at him. "Of course. Humans recollecting any of these events would only mean trouble in the end."

Magneto nodded. "Then I will leave you to your good work Harkness. Till we meet again."

The Master of Magnetism glanced once more to his daughter, and the fresh tears on her face. As a father, he should feel terrible about tearing his only daughter away from her family to live in a cell, but he didn't feel that at all.

If anything, an emotion similar to pride arose in him.

He, an Omega-level Homo-superior, was pushed to lock his own daughter away simply because she did not have a proper control over her abilities, and she was only four! From this moment on, she can only ascend in her powers and become the symbol of mutantkind's future, one that was born broken and abused, only to rise strong and victorious.

"Another thing, Harkness." He suddenly spoke out.

The old woman stared at him from the corner of her eyes, a signal that she was listening.

"Charles is not to know of Wanda's existence and whereabouts under any circumstances."

The sorceress nodded. "I shall do what I can."

* * *

Many days had passed since that fateful evening, and containing Wanda's power without confronting her in a physical sense had been very tricky for Agatha, but the Salem Witch was a resourceful one. She had managed, and persevered.

"And you say that he locked his own daughter away?"

The witch brought herself out of her own thoughts to face the guest of her simple abode. A woman very much like herself, crafty, ruthless when necessary, and one who's willing to do the necessary deed.

"Yes Raven, though I have expressed my conflictions about it, he did not seem to listen to any reason other than his own."

Mystique looked down as her mind thought of many conceived plans with the Maximoff child.

"This girl….she can be very useful for _my_ plans."

Harkness narrowed her eyes at the woman, "I was under the impression that you and Magnus were pursuing the same goal, why conspire against him so?"

"Don't be ridiculous Agatha, Magnus is the savior and leader of the mutant race, it's his destiny to bring us to a brighter future," Mystique replied casually before her eyes took a darker tone. "Unfortunately, he took something from me…something irreplaceable, and I will make sure he doesn't achieve that future without some cost."

She stared straight at the old woman, as if daring her to say something, but Agatha did not speak out. It was not her problem, she was not a pawn of Magneto.

Besides….. there truly is no wrath compared to a mother's wrath.

Suddenly, one of the magical barriers Agatha placed went off, like a fire siren. Specifically the one in Ravencroft, but that was not right. The only thing that can set it off-

"Excuse me Raven, but I must leave." She said briskly as she stood and reached for her cane.

"Trouble?" Mystique questioned.

"I shall see. I hate to be a rude guest, but I would kindly ask you to see yourself out now." Harkness stamped twice on the ground before she swirled away in a purple vortex.

She reappeared in a corner at the Ravencroft Mental Institute. When she left the corner, she found three children huddled around a man confined to a wheelchair.

"Charles." She greeted.

Xavier looked up and instantly recognized the elderly woman as walked quickly to the group.

"Agatha! It has been a long time. I'm certain that you haven't met these three? Naruto, Scott, Jean, this is Agatha Harkness, an old friend of mine."

"Professor, how do you know each other?" Scott asked meekly.

Naruto huffed, "Old people always know each other, Scott. That's what I learned."

Xavier could only sigh, apparently this Naruto character had called him old for a very long time.

"Charles, even though it is good to see you in good health, I'm afraid that you cannot proceed any further." Harkness replied.

"Really?" Xavier replied with interest, "and who would tell you to do that?"

Agatha did not reply.

"Well if it's all the same to you, I would very much like to meet this person who wishes to stop me from meeting…..Wanda, is it? Until then, I believe I have every right to visit her as her new psychologist."

"Then I must stop you." Agatha replied firmly, she twiddled her old fingers, getting them fluid enough to cast spells should Xavier ever become openly hostile.

"There is no need for violence."

Harkness stopped. It was a new voice, one she hadn't recognized. Out came a man, his face resembled of Asian descent, and he wore a black trench coat over plan white clothing, but it was the amulet he wore that nearly stopped Agatha's heart.

"Miss Harkness, I don't think I've ever had the privilege of introducing you to my friend, Wong. It was a coincidence that we ran into each other in New York. He holds much interest in young Wanda as I do."

Agatha stiffly nodded her head. "A pleasure to meet a pupil of the Ancient One."

Wong nodded, "It is an honor to meet a sorceress of your wisdom and age. Please, allow my friend to visit this young one."

The choice was very simple. Agatha was very old a powerful, but her capabilities was a mere candle to that of the man who locked Dormanmu away.

There was a reason that he was called the Sorcerer Supreme, and he would no doubt take only the best of pupils.

The woman slowly resumed her casual stance, "Very well. I did promise I would do the best I can, and this is clearly beyond me."

She returned to the shadows and silently disappeared.

Wong turned around and spoke to Xavier. "I'm afraid that our journey ends here Charles. I have sensed her capabilities already. She's certainly strong, but her fear makes her dangerous to us. The Ancient One and I feel that she may grow well in better hands, your hands."

Xavier nodded. "Thank you for your help, old friend."

"See? Even the old man called him old!" Naruto pointed out.

Wong smiled at the boy, then left out the door without another word.

"Now, she is a little scared, so it might be prudent that someone around her age would greet her first. We can only go one at a time, so who would like to go first?"

Each other three children all looked at each other with uncertainty. Jean was the one who was the most afraid. Like the Professor, she could feel the emotions that Wanda was giving out and they were very potent, it warded Jean away in fear.

Scott had noticed Jean's discomfort, it made him uncomfortable as well. Somehow, he quickly got a notion that whatever made the red head unhappy was not good news.

Naruto stared at both of them, at their distress, and that made him mad. Nothing was gonna scare his new friends under his watch!

"I'll go!" He declared.

Xavier didn't ask him if he was certain or if he even wanted to reconsider. In fact, he smiled.

"Here's a chessboard, and inside are checkers. Why don't you play a game or two with her, get to know her a bit?"

* * *

 **AND WE'RE DONE!**

 **Sorry for the abrupt end, but my head was hurting!**

 **Wow, talk about Xavier having friends in high places, and what higher is there than the Sorcerer Supreme?**

 **Obviously, I'm trying to bring the entirety of the Marvel Universe into this fanfic because hey, Xavier lives in New York, the center of all the Marvel Superheroes!**

 **So, I've decided that the Scarlet Witch become an X-Man! Why you ask? Because that will be the first step to becoming an Avenger!**

 **So you'd like the introductions for Wolverine and Storm? It's as comic historically accurate as I can make it.**

 **Anyway, Review for QUESTIONS, COMMENTS, COMPLAINTS, AND CONCERNS!**

 **Though I won't be able to answer since I have to be off the Internet.**

 **MAY THE FLAMES OF YOUTH BE WITH YOU, ALWAYS.**


	4. Chapter 4: Day 1

**Hi again! This is the Phantom Penance's triumphant return!**

 **Sorry that I was gone for the whole month of August. It was a pure and holy blend of religious soul searching and procrastination, I had to whip myself back into shape in order to get back to work.**

 **Anyway, welcome to another Chapter of Shinobi: Second Evolution!**

 **I have to work my way down with my stories before I get to the major ones like Hero or Assassin and/or Kings of gods.**

 **So let's make another chapter, ne?**

 **Also, in case you haven't noticed already:**

 **DISCLAIMER: I OWN EVERY-JUST KIDDING, I OWN NOTHING 'CEPT THE HAIRS ON MY BEAUTIFUL HEAD**

 **Chapter 4: Day 1 Of The Rest Of Their Lives**

* * *

 _(Xavier's Institute of Higher Learning: Year 1 ½_

 _Occupants: 4)_

"Hold it still, Jean!" Scott yelled out as he concentrated on his own task.

The red head grew a tick mark in annoyance. "You probably haven't noticed it yet, Scott, but I'm holding a desk up in the air with sheer willpower alone. Can you-oh, I don't know-be a little patient!?"

"I can't get a proper shot if you keep moving. Besides, you're doing great," the boy exclaimed back.

On top of that desk was a stack of books, and on that stack, was a single clay disk that needed to be hit by something of high caliber, like a shotgun shell or an optic blast.

It was a new training sequence that Xavier had thoughtfully set up, one that combined precision, stamina, and teamwork. Jean had to hold the desk in the air long and steady, long enough until Scott is confident that he could make the shot from a reflecting mirror.

It was endearing work because neither of them were very patient.

"You keep raising it higher, I won't make it at that height!"

"What are you talking about, this is as high as I can go!"

"Well, unless the desk is magically lifting itself-"

"You know what, let's switch jobs! You can hold the desk with your mind, and I can shoot-"

'There!' Scott practically yelled in his mind. It took a split second to turn off his brand new visor and fire that dangerous power of the sun harnessed in his eyes, the blast ricocheted off the mirror. The blast soared in an angle till it struck the clay disk right in the middle.

The brown haired boy smirked. "Straight in the middle. A perfect bullseye."

"Don't tell me you had me hold up a desk for over half an hour just so you can get a bullseye." Jean frowned with her arms crossed.

"Yeah, sorry. You did great, by the way. Definitely improving." Scott encouraged quickly, lest he face the fearsome wrath of a redhead. A telepathic redhead at that.

Jean huffed. "Darn right, I am." Her prideful face then softened as she spoke mostly to herself. "I wonder what Naruto's doing right now."

That was when Scott's uneasy face turned to one of a childish jealousy, but he never dared showed it in front of Jean.

"Why wonder? He's with her doing whatever the Professor wants him to do."

"Oh, come off it!" Grey demanded as she ruthlessly hit Scott in the shoulder. "The Professor doesn't have favorites, we're all equally his students."

"He grew up with the Professor, sure, but that isn't a good excuse," Scott insisted in the form of a grumble, "We should be doing this together."

"Just admit he's better at using his abilities than us, that's why he trains at a different level. Besides, his powers are pretty simple compared to ours." Jean replied, but then she turned her head towards the Institute as her over-imaginative thoughts began to get the better of her.

"I wonder what level of intensity Naruto's training is now. With his strength, he could be lifting semis at this very moment and we wouldn't even know…."

* * *

(Inside Xavier's Institute of Higher Learning)

' _You put the lime in the coconut and drink it all up, you put the lime in the coconut and drink it all up, you put the lime in the coconut and drink it all up, you put the lime in the coconut and drink it all up, you put the lime-'_

"Checkmate." Those words brought the boy out of his mental song and double-check is forces, or lack thereof.

"Eh? What!? That's not possible, you were cheating again! Admit it!"

"I wasn't cheating. You weren't paying attention," his opponent replied in amusement.

"Yeah, wasn't paying attention to you cheating! I knew what I was doing!"

"Of course, so then you knew you were losing."

While Naruto and Wanda were having an argument, Charles could only sigh. It would seem that even though Naruto could process information better than any human alive, that potential was incredibly limited by his very short attention span.

It seems that he can get too distracted to formulate a long-term plan of attack. If Xavier was planning to make a team of mutants that would be a beacon of the future for both mutants and humans, then there's a good chance that Naruto will not be leading it.

"Old man X, tell me that Wanda was cheating. She had to be cheating, right?" Naruto insisted.

Charles checked the chessboard to see that the king was completely surrounded, as in, the king piece was in a circle made of assorted chess pieces.

One would have to really not pay attention to the game in order to let that happen.

"…..She has undoubtedly checkmated you."

"AW C'MON!"

The spiky blonde haired child began arguing with Wanda anew, leaving both Wanda and Charles to smile at his stubbornness.

Speaking of which, Wanda has taken many great strides in improving from her short yet terrifying experience at Ravencroft. Her hair, once a dark black, had transformed into a healthy shade of brown as well as it had grown in length. She was pale white in the face and skin, but now she was tanned and very rosy.

It seemed like life itself had breathed into the girl at the Institute.

Also, after a hard year and a half of practicing, Wanda was now happy to declare that she can turn off and on her mutant abilities, a genuine milestone considering that her original problem was having a complete lack of control.

But, as stated before, those days were water under the bridge now.

"See? I knew he wasn't doing an exercise at all!" Scott loudly accused as the two entered the room. His just reward was getting another shove in the elbow by Jean before both of them got caught up in a massive bear hug.

"You guys done already, awesome! I knew you guys could do it!" Naruto exclaimed.

Scott grumbled in the blonde's vice-like grip while Jean flushed in embarrassment, an act Wanda paid close attention to. It interested her, watching a normally tan face swell red in a matter of moments, perhaps her perception of such things will change when she is older and more concerned about social affairs…

"Well, now that you are all finished, I believe it is time for your next training simulation." Xavier cheerfully declared.

"Mwah, no more chess games!" Naruto wailed.

"And not two on two! We need to train together," Scott insisted in a heartbeat.

The bald Professor's smile brightened even more, "Then you will both be very pleased with the session I have in mind."

* * *

"Old man, care to explain why we're being forced to wear jumpsuits, black jumpsuits at that!" Naruto yelled out as he and Scott changed into black, skin tight, suits. He could only assume that Jean and Wanda were doing the same in the other locker.

" _Those 'jumpsuits' are a special fabric me and Dr. MacTaggert have constructed. They are durable to the elements and so far, won't inhibit you in any form or fashion of using your powers."_ Xavier replied over the intercoms.

"But they're black!" Naruto moaned. "It's not as cool as orange!"

"Orange technically is a vibrant color in the spectrum, Naruto." Scott spoke up, "but still, beats plain black."

" _Very well, I'll let you customize them if you insist so."_

The duo finished changing into their training gear and entered a complete Danger Room obstacle course, filled with holographic uphills and downhills, thought that may not be all that simple with the Danger Room.

Jean stared at her suit in discontent. "It _itches_ , and sticks to my skin a lot."

Wanda nodded in agreement, "It isn't comfortable in the least."

" _Apologies, but your safety vastly outweighed your personal comfort at the time these suits were being made."_ Xavier's voice boomed through the intercoms of the Danger Room.

"So what are we doin' X?" Naruto yelled back.

" _The exercise is simple, capture the flag."_ As he said that, a massive column with a red flag ontop rose to the ceiling at the other end of the Danger Room.

" _You are free to reach the flag in your own way as well as deal with the obstacles however you see fit, but all four of you must reach the flag together. And as usual, you will be timed."_ Xavier instructed.

To prove his point, a giant stopwatch appeared above the entire room, and it was counting down from 5.

Scott sighed, someone had to take command, and someone had to take it right now. "Alright, the first thing we should is stick together and-"

"EVERY MAN FOR HIMSELF!"

They all stared dumbfounded, as Naruto nearly ran half a mile in a few seconds, then he turned around and looked at them.

"Don't just stand there! Last one to the flag is a rotten egg!" He excitedly yelled.

Before the optical-mutant could even let out a syllable, Naruto was already speeding his way through the course with reckless abandon. He smashed his way through walls and boulders alike in high sense of glee, nearly in psychotic proportions.

Jean patted Scott's back in sympathy. "I thought your plan was going to be great Scott, but how about we follow the path Naruto's making for us?"

Scott sniffed as he mourned the passing of his opportunity. "….Yeah. Let's use him as a bulldozer."

* * *

"Ha Ha! Fear me, you puny weapons!" Naruto yelled in triumph as he barreled up the hill that stretched before him.

A massive turrent underneath the ground rose up and pointed its guns straight at the boy. Naruto ducked behind a boulder as the machine laid a suppressive fire of non-lethal bullets. The blonde was grinning with glee at the new fun he was having, this was what he lived for!

Suddenly, a red beam streaked past his head and struck the turrent. The machine exploded with fire and sparks as Naruto turned behind him to see Scott, Jean, and Wanda catching up to him. The first name he mentioned was holding his visors as the red in them powered down.

"Glad you can keep up!" Naruto exclaimed with excitement. "Man Scott, you use those new visors really good-"

Wanda stomped towards the grinning blonde and slapped him straight over his head, making Naruto yell out in pain and confusion.

"Wuh-Why did you do that, Wanda?" The boy sniffed while holding his forehead fondly.

"That is your punishment for running off like a delinquent!" The brunette sharply responded. "Have you learned nothing in chess? No chess piece is to be used recklessly, and you were the definition of recklessness!"

Jean spoke, albeit a bit reluctantly. "Wanda's right, Naruto, though I wouldn't be so harsh about it. We're supposed to do this together, like a real team."

"But it's not as fun!" Naruto pouted.

"It's not supposed to be fun, it's supposed to be training." Scott replied. "Whatever you do alone is on you, but when we're together, we got to do what Professor Xavier says and work like a team."

Naruto still had his arms folded, but once he looked at the faces of his new friends, his new precious people, he slowly saw things differently. Wanda, Scott, and Jean clearly saw this as something different than fun, they needed his support and he was being a jerk sitting on the ground, pouting.

The whiskered child with the strange eyes stared a moment longer, then sighed. Very well, he will submit to them.

 _For now._

"Fine, fine, fine, fine, fine, you didn't have to hit me on the head though. Could've just told me…." He mumbled.

Jean sighed, relieved that things hadn't broken out into some sort of disagreement.

"So, what are we gonna do now?" She asked.

Naruto sheepishly grinned while he rubbed his head. "I was gonna run up to the top, but since you guys are with me…new plan!"

"We'll go together." Scott cut in. "Let's just stay close to each other, that way, we can handle anything that the Professor throws at us easily."

Both Wanda and Jean nodded enthusiastically at Scott's plan, but for some reason, Naruto just huffed and stared at the visor-wearing boy from the corner of his eye.

"…Yeah sure, that's okay…I guess."

* * *

Charles widened his eyes in surprised and zoomed in on a sight he did not think he would see so soon.

' _So, it seems that Scott was natural born leader among them the entire time. It was foolish of me to favor one of my student's abilities over the others.'_ He thought with pride.

His screen showed all four of his students working together, making a square formation that brought them closer and closer to the flag. With Naruto in the front so that he would take care of the obstacles in the way, Scott right beside him, unleashing optic blasts while yelling inaudible orders.

Wanda was on Naruto's other side, using her very limited abilities to just destroy objects while Jean stayed in the middle, using her telekinesis form a shield against small things like pellets and debris.

The simulation ended with Naruto giving them all a bear hug with a huge grin, Jean appearing to be flustered, Wanda was flashing a small smile, and Scott suffocating in Naruto's embrace, but holding a giant red flag for the impaired Professor to see.

"Little by little, piece by piece, a brighter future is becoming visible." He declared as he turned off the simulation and prepared to give them their report.

* * *

 _(Undisclosed Location)_

A new future.

A brighter future was what everybody wanted, but unfortunately, only the superior race was going to get it, and the monstrous humans would face judgement.

However, such things were momentarily placed on a shelf as instantaneous judgement had to be carried out on a certain witch.

"I gave you a simple request," Magnus began, "control Wanda and keep her from Charles, and yet you failed at both! Explain yourself, Harkness!"

Agatha Harkness stared at the Master of Magnetism unflinchingly, she didn't even give Magnus the pleasure of seeing her fear at the flailing metal that threatened to wrap tightly around her body, being held back only by Magneto who was slipping into a murderous rage.

"I have done exactly what you asked of me. With my power, Charles Xavier would have never known that Wanda Maximoff had existed."

"Then why is she with _him_ now!?" Magneto demanded.

"With all my sorcery and strength, I am nothing compared to the Sorcerer Supreme who accompanied Charles." She answered.

Magnus narrowed his eyes at the woman. "I thought you said his pupil was with Charles, not the sorcerer himself."

"Wong is still much more knowledgeable in the mystic arts than I am. He tends to the arcane tomes and enchantment books." Agatha replied.

Magneto growled as he turned away from the woman who took it her permission to leave in a wisp of black smoke.

He sat on his metal throne in deep thought, something that Mystique took it upon herself to make sure that never happened. If there was anything that caused the savior of the mutant race to think, it should be something that Mystique has already taken care of. Period.

"Magnus, I can sneak into the Mansion and steal the girl-"

"That would not be wise, Raven."

Both turned to the voice of the older woman who came down the stairs. You could tell she was old by the natural gray color of her hair, but her body still had the womanly curves of a younger woman, and her eyes were concealed by a pair of dark glasses.

"And why is that, Destiny?" Magneto questioned.

"Wanda has an important role to play in the Mansion, one that was not clear to me until recently." Destiny responded.

"However, she will return to us soon enough, that much I can see. In the meantime, Raven, you must go to Mississippi. A young child there is in search of mutant guidance. Eric, there is a visitor at the door whom you must attend to."

Magneto raised an eyebrow as the two women left through the back door, giving the Master of Magnetism some much needed privacy. Through the use of his abilities, he willed the door to open, letting in a man.

No, not much of a man, a beast.

He was taller than most men, and more hairy too. However, he possessed sharpened claws, deadly fangs, and the eyes of predator, in constant need of bloodshed.

"You are clearly one of the homo-superior," Magnus stated the ever obvious. "Why have you come here?"

"I hear you're looking for someone who ain't afraid to do some dirty work. Get a little blood in their food." The man spoke harshly, as harsh as his demeanor showed him to be.

Magneto looked straight into the creature's eye, devoid of hesistation, of weakness. "Indeed I am. Are you a man of such talents?"

The man-beast stared at Magneto, then gave a deep and menacing laugh. "Bub, look no further than Sabretooth here. I practically _bathe_ in it."

* * *

 **Chapter Four Completed!**

 **It's certainly been a while, hasn't it? I'm not gonna lie, I got a little complacent in the September month, and all these new Senior expectations are blowing fuses in my head.**

 **I gotta pass the SAT/ACTs, get some scholarships, find what colleges I want to go to,** _ **apply**_ **to those colleges, it'll drive me mad or get me a heart attack on worrying.**

 **Anyway, there's some Naruto/Scott animosity going on! It's not clear, but someone likes someone, and it certainly isn't helping that Xavier's taking sides prematurely. Then there's the case of Wanda, is she really going to rejoin her father after what he'd done to her?**

 **Sabretooth, Destiny, Wong and the Ancient One, this certainly is a chapter of beginnings, isn't it?**

 **IMPORTANT RIGHT HERE!**

 **If you know what's good for you, you'll go to my profile and check out the poll I made! It's for who's going to be Naruto's long lasting pairings! It won't be a permanent pairing because Naruto won't stay on Earth and some people may die, but here are the choice:**

 **Scarlet Witch**

 **Jean Grey**

 **Emma Frost**

 **Veranke**

 **Brood Queen**

 **Madelyne Pryor**

 **Crystal (From the Inhumans)**

 **X-23 Laura Kinney**

 **Rogue**

 **Anyway, go to my profile and vote! Naruto's love life is depending on it! And as always.**

 **MAY THE FLAMES OF YOUTH BE WITH YOU, ALWAYS.**


End file.
